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flye.log

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  1. [2024-08-27 13:42:20] root: INFO: Starting Flye 2.9.3-b1797
    2. 

  2. [2024-08-27 13:42:20] root: DEBUG: Cmd: /data/tools/Flye/bin/flye --nano-hq output_7.fasta -o tmp_7
    3. 

  3. [2024-08-27 13:42:20] root: DEBUG: Python version: 3.8.10 (default, Nov 22 2023, 10:22:35) 
    4. 

  4. [GCC 9.4.0]
    5. 

  5. [2024-08-27 13:42:20] root: INFO: >>>STAGE: configure
    6. 

  6. [2024-08-27 13:42:20] root: INFO: Configuring run
    7. 

  7. [2024-08-27 13:42:20] root: INFO: Total read length: 117213
    8. 

  8. [2024-08-27 13:42:20] root: INFO: Reads N50/N90: 8239 / 4347
    9. 

  9. [2024-08-27 13:42:20] root: INFO: Minimum overlap set to 4000
    10. 

  10. [2024-08-27 13:42:20] root: INFO: >>>STAGE: assembly
    11. 

  11. [2024-08-27 13:42:20] root: INFO: Assembling disjointigs
    12. 

  12. [2024-08-27 13:42:20] root: DEBUG: -----Begin assembly log------
    13. 

  13. [2024-08-27 13:42:20] root: DEBUG: Running: flye-modules assemble --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_7.fasta --out-asm /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/00-assembly/draft_assembly.fasta --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/flye.log --threads 1 --min-ovlp 4000
    14. 

  14. [2024-08-27 13:42:20] DEBUG: Build date: May 16 2023 00:48:26
    15. 

  15. [2024-08-27 13:42:20] DEBUG: Total RAM: 503 Gb
    16. 

  16. [2024-08-27 13:42:20] DEBUG: Available RAM: 420 Gb
    17. 

  17. [2024-08-27 13:42:20] DEBUG: Total CPUs: 160
    18. 

  18. [2024-08-27 13:42:20] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg
    19. 

  19. [2024-08-27 13:42:20] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg
    20. 

  20. [2024-08-27 13:42:20] DEBUG: 	big_genome_threshold=29000000
    21. 

  21. [2024-08-27 13:42:20] DEBUG: 	meta_read_filter_kmer_freq=100
    22. 

  22. [2024-08-27 13:42:20] DEBUG: 	chain_large_gap_penalty=2
    23. 

  23. [2024-08-27 13:42:20] DEBUG: 	chain_small_gap_penalty=0.5
    24. 

  24. [2024-08-27 13:42:20] DEBUG: 	chain_gap_jump_threshold=100
    25. 

  25. [2024-08-27 13:42:20] DEBUG: 	max_jump_gap=500
    26. 

  26. [2024-08-27 13:42:20] DEBUG: 	max_coverage_drop_rate=5
    27. 

  27. [2024-08-27 13:42:20] DEBUG: 	max_extensions_drop_rate=5
    28. 

  28. [2024-08-27 13:42:20] DEBUG: 	chimera_window=100
    29. 

  29. [2024-08-27 13:42:20] DEBUG: 	chimera_overhang=1000
    30. 

  30. [2024-08-27 13:42:20] DEBUG: 	min_reads_in_disjointig=4
    31. 

  31. [2024-08-27 13:42:20] DEBUG: 	max_inner_reads=10
    32. 

  32. [2024-08-27 13:42:20] DEBUG: 	max_inner_fraction=0.25
    33. 

  33. [2024-08-27 13:42:20] DEBUG: 	aggressive_dup_filter=1
    34. 

  34. [2024-08-27 13:42:20] DEBUG: 	max_separation=500
    35. 

  35. [2024-08-27 13:42:20] DEBUG: 	unique_edge_length=50000
    36. 

  36. [2024-08-27 13:42:20] DEBUG: 	min_repeat_res_support=0.51
    37. 

  37. [2024-08-27 13:42:20] DEBUG: 	out_paths_ratio=5
    38. 

  38. [2024-08-27 13:42:20] DEBUG: 	graph_cov_drop_rate=5
    39. 

  39. [2024-08-27 13:42:20] DEBUG: 	coverage_estimate_window=100
    40. 

  40. [2024-08-27 13:42:20] DEBUG: 	max_bubble_length=50000
    41. 

  41. [2024-08-27 13:42:20] DEBUG: 	loop_coverage_rate=1.5
    42. 

  42. [2024-08-27 13:42:20] DEBUG: 	repeat_edge_cov_mult=1.75
    43. 

  43. [2024-08-27 13:42:20] DEBUG: 	weak_detach_rate=5
    44. 

  44. [2024-08-27 13:42:20] DEBUG: 	tip_coverage_rate=2
    45. 

  45. [2024-08-27 13:42:20] DEBUG: 	tip_length_rate=2
    46. 

  46. [2024-08-27 13:42:20] DEBUG: 	output_gfa_before_rr=1
    47. 

  47. [2024-08-27 13:42:20] DEBUG: 	remove_alt_edges=0
    48. 

  48. [2024-08-27 13:42:20] DEBUG: 	low_cutoff_warning=0
    49. 

  49. [2024-08-27 13:42:20] DEBUG: 	kmer_size=17
    50. 

  50. [2024-08-27 13:42:20] DEBUG: 	use_minimizers=1
    51. 

  51. [2024-08-27 13:42:20] DEBUG: 	minimizer_window=10
    52. 

  52. [2024-08-27 13:42:20] DEBUG: 	reads_base_alignment=1
    53. 

  53. [2024-08-27 13:42:20] DEBUG: 	meta_read_top_kmer_rate=0.75
    54. 

  54. [2024-08-27 13:42:20] DEBUG: 	maximum_jump=1500
    55. 

  55. [2024-08-27 13:42:20] DEBUG: 	maximum_overhang=1500
    56. 

  56. [2024-08-27 13:42:20] DEBUG: 	repeat_kmer_rate=100
    57. 

  57. [2024-08-27 13:42:20] DEBUG: 	assemble_ovlp_divergence=0.05
    58. 

  58. [2024-08-27 13:42:20] DEBUG: 	assemble_divergence_relative=1
    59. 

  59. [2024-08-27 13:42:20] DEBUG: 	repeat_graph_ovlp_divergence=0.05
    60. 

  60. [2024-08-27 13:42:20] DEBUG: 	read_align_ovlp_divergence=0.10
    61. 

  61. [2024-08-27 13:42:20] DEBUG: 	hpc_scoring_on=1
    62. 

  62. [2024-08-27 13:42:20] DEBUG: 	add_unassembled_reads=0
    63. 

  63. [2024-08-27 13:42:20] DEBUG: 	extend_contigs_with_repeats=0
    64. 

  64. [2024-08-27 13:42:20] DEBUG: 	min_read_cov_cutoff=3
    65. 

  65. [2024-08-27 13:42:20] DEBUG: 	short_tip_length=20000
    66. 

  66. [2024-08-27 13:42:20] DEBUG: 	long_tip_length=100000
    67. 

  67. [2024-08-27 13:42:20] DEBUG: Running with k-mer size: 17
    68. 

  68. [2024-08-27 13:42:20] DEBUG: Running with minimum overlap 4000
    69. 

  69. [2024-08-27 13:42:20] DEBUG: Metagenome mode: N
    70. 

  70. [2024-08-27 13:42:20] DEBUG: Short mode: N
    71. 

  71. [2024-08-27 13:42:20] INFO: Reading sequences
    72. 

  72. [2024-08-27 13:42:20] DEBUG: Building positional index
    73. 

  73. [2024-08-27 13:42:20] DEBUG: Total sequence: 113554 bp
    74. 

  74. [2024-08-27 13:42:20] INFO: Building minimizer index
    75. 

  75. [2024-08-27 13:42:20] INFO: Pre-calculating index storage
    76. 

  76. [2024-08-27 13:42:20] DEBUG: Mean k-mer frequency: 3.72347
    77. 

  77. [2024-08-27 13:42:20] DEBUG: Repetitive k-mer frequency: 372
    78. 

  78. [2024-08-27 13:42:20] DEBUG: Filtered 0 repetitive k-mers (0)
    79. 

  79. [2024-08-27 13:42:20] INFO: Filling index
    80. 

  80. [2024-08-27 13:42:20] DEBUG: Sorting k-mer index
    81. 

  81. [2024-08-27 13:42:20] DEBUG: Selected k-mers: 5492
    82. 

  82. [2024-08-27 13:42:20] DEBUG: K-mer index size: 20453
    83. 

  83. [2024-08-27 13:42:20] DEBUG: Mean k-mer frequency: 3.72414
    84. 

  84. [2024-08-27 13:42:20] DEBUG: Minimizer rate: 5.55195
    85. 

  85. [2024-08-27 13:42:20] DEBUG: Peak RAM usage: 0 Gb
    86. 

  86. [2024-08-27 13:42:20] DEBUG: Estimating k-mer identity bias
    87. 

  87. [2024-08-27 15:43:17] DEBUG: Initial divergence estimate : 0.0111658
    88. 

  88. [2024-08-27 15:43:17] DEBUG: Relative threshold: Y
    89. 

  89. [2024-08-27 15:43:17] DEBUG: Max divergence threshold set to 0.0611658
    90. 

  90. [2024-08-27 15:43:17] INFO: Extending reads
    91. 

  91. [2024-08-27 15:43:17] DEBUG: Estimating overlap coverage
    92. 

  92. [2024-08-27 15:44:44] INFO: Overlap-based coverage: 9
    93. 

  93. [2024-08-27 15:44:44] INFO: Median overlap divergence: 0.0122304
    94. 

  94. [2024-08-27 15:44:44] DEBUG: Sequence divergence distribution: 
    95. 

  95. 

  96.     |  *         |                                                                                       
    97. 

  97.     |  *         |                                                                                       
    98. 

  98.     |  *         |                                                                                       
    99. 

  99.     |  *         |                                                                                       
    100. 

  100.     |  *         |                                                                                       
    101. 

  101.     |  *         |                                                                                       
    102. 

  102.     |  *         |                                                                                       
    103. 

  103.     |  *         |                                                                                       
    104. 

  104.     |  *         |                                                                                       
    105. 

  105.     |  *         |                                                                                       
    106. 

  106.     | **         |                                                                                       
    107. 

  107.     | **         |                                                                                       
    108. 

  108.     | **         |                                                                                       
    109. 

  109.     |****        |                                                                                       
    110. 

  110.     |****        |                                                                                       
    111. 

  111.     |****        |                                                                                       
    112. 

  112.     |*****       |                                                                                       
    113. 

  113.     |*****       |                                                                                       
    114. 

  114.     |*****       |                                                                                       
    115. 

  115.     |*****       |                                                                                       
    116. 

  116.     ----------------------------------------------------------------------------------------------------
    117. 

  117.     0%        5%        10%       15%       20%       25%       30%       35%       40%       45%       
    118. 

  118. 

  119.     Q25 = 0.0094, Q50 = 0.012, Q75 = 0.015
    120. 

  120. 

  121. [2024-08-27 15:44:44] DEBUG: Assembled disjointig 1
    122. 

  122. 	With 6 reads
    123. 

  123. 	Start read: +56bbfd4a-0d1d-4d97-b307-7626be446ce8
    124. 

  124. 	At position: 4
    125. 

  125. 	leftTip: 1 rightTip: 1
    126. 

  126. 	Suspicious: 4
    127. 

  127. 	Short ext: 1
    128. 

  128. 	Mean extensions: 2
    129. 

  129. 	Avg overlap len: 5205
    130. 

  130. 	Min overlap len: 3173
    131. 

  131. 	Inner reads: 0
    132. 

  132. 	Length: 20431
    133. 

  133. [2024-08-27 15:44:44] DEBUG: Inner: 24 covered: 28 total: 28
    134. 

  134. [2024-08-27 15:46:08] INFO: Assembled 1 disjointigs
    135. 

  135. [2024-08-27 15:46:08] INFO: Generating sequence
    136. 

  136. [2024-08-27 15:46:08] DEBUG: Building positional index
    137. 

  137. [2024-08-27 15:46:08] DEBUG: Total sequence: 20417 bp
    138. 

  138. [2024-08-27 15:46:08] DEBUG: Mean k-mer frequency: 1.00241
    139. 

  139. [2024-08-27 15:46:08] DEBUG: Repetitive k-mer frequency: 100
    140. 

  140. [2024-08-27 15:46:08] DEBUG: Filtered 0 repetitive k-mers (0)
    141. 

  141. [2024-08-27 15:46:09] DEBUG: Sorting k-mer index
    142. 

  142. [2024-08-27 15:46:09] DEBUG: Selected k-mers: 3738
    143. 

  143. [2024-08-27 15:46:09] DEBUG: K-mer index size: 3748
    144. 

  144. [2024-08-27 15:46:09] DEBUG: Mean k-mer frequency: 1.00268
    145. 

  145. [2024-08-27 15:46:09] DEBUG: Minimizer rate: 5.44744
    146. 

  146. [2024-08-27 15:46:09] INFO: Filtering contained disjointigs
    147. 

  147. [2024-08-27 15:46:09] DEBUG: Computing transitive closure for overlaps
    148. 

  148. [2024-08-27 15:46:09] DEBUG: Found 0 overlaps
    149. 

  149. [2024-08-27 15:46:09] DEBUG: Left 0 overlaps after filtering
    150. 

  150. [2024-08-27 15:46:09] INFO: Contained seqs: 0
    151. 

  151. [2024-08-27 15:46:09] DEBUG: Writing FASTA
    152. 

  152. [2024-08-27 15:46:09] DEBUG: Peak RAM usage: 0 Gb
    153. 

  153. -----------End assembly log------------
    154. 

  154. [2024-08-27 15:46:09] root: DEBUG: Disjointigs length: 20417, N50: 20417
    155. 

  155. [2024-08-27 15:46:09] root: INFO: >>>STAGE: consensus
    156. 

  156. [2024-08-27 15:46:09] root: INFO: Running Minimap2
    157. 

  157. [2024-08-27 15:46:09] root: INFO: Computing consensus
    158. 

  158. [2024-08-27 15:46:09] root: INFO: Alignment error rate: 0.008460
    159. 

  159. [2024-08-27 15:46:09] root: INFO: >>>STAGE: repeat
    160. 

  160. [2024-08-27 15:46:09] root: INFO: Building and resolving repeat graph
    161. 

  161. [2024-08-27 15:46:09] root: DEBUG: -----Begin repeat analyser log------
    162. 

  162. [2024-08-27 15:46:09] root: DEBUG: Running: flye-modules repeat --disjointigs /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/10-consensus/consensus.fasta --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_7.fasta --out-dir /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/20-repeat --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/flye.log --threads 1 --min-ovlp 4000
    163. 

  163. [2024-08-27 15:46:09] DEBUG: Build date: May 16 2023 00:48:44
    164. 

  164. [2024-08-27 15:46:09] DEBUG: Total RAM: 503 Gb
    165. 

  165. [2024-08-27 15:46:09] DEBUG: Available RAM: 420 Gb
    166. 

  166. [2024-08-27 15:46:09] DEBUG: Total CPUs: 160
    167. 

  167. [2024-08-27 15:46:09] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg
    168. 

  168. [2024-08-27 15:46:09] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg
    169. 

  169. [2024-08-27 15:46:09] DEBUG: 	big_genome_threshold=29000000
    170. 

  170. [2024-08-27 15:46:09] DEBUG: 	meta_read_filter_kmer_freq=100
    171. 

  171. [2024-08-27 15:46:09] DEBUG: 	chain_large_gap_penalty=2
    172. 

  172. [2024-08-27 15:46:09] DEBUG: 	chain_small_gap_penalty=0.5
    173. 

  173. [2024-08-27 15:46:09] DEBUG: 	chain_gap_jump_threshold=100
    174. 

  174. [2024-08-27 15:46:09] DEBUG: 	max_jump_gap=500
    175. 

  175. [2024-08-27 15:46:09] DEBUG: 	max_coverage_drop_rate=5
    176. 

  176. [2024-08-27 15:46:09] DEBUG: 	max_extensions_drop_rate=5
    177. 

  177. [2024-08-27 15:46:09] DEBUG: 	chimera_window=100
    178. 

  178. [2024-08-27 15:46:09] DEBUG: 	chimera_overhang=1000
    179. 

  179. [2024-08-27 15:46:09] DEBUG: 	min_reads_in_disjointig=4
    180. 

  180. [2024-08-27 15:46:09] DEBUG: 	max_inner_reads=10
    181. 

  181. [2024-08-27 15:46:09] DEBUG: 	max_inner_fraction=0.25
    182. 

  182. [2024-08-27 15:46:09] DEBUG: 	aggressive_dup_filter=1
    183. 

  183. [2024-08-27 15:46:09] DEBUG: 	max_separation=500
    184. 

  184. [2024-08-27 15:46:09] DEBUG: 	unique_edge_length=50000
    185. 

  185. [2024-08-27 15:46:09] DEBUG: 	min_repeat_res_support=0.51
    186. 

  186. [2024-08-27 15:46:09] DEBUG: 	out_paths_ratio=5
    187. 

  187. [2024-08-27 15:46:09] DEBUG: 	graph_cov_drop_rate=5
    188. 

  188. [2024-08-27 15:46:09] DEBUG: 	coverage_estimate_window=100
    189. 

  189. [2024-08-27 15:46:09] DEBUG: 	max_bubble_length=50000
    190. 

  190. [2024-08-27 15:46:09] DEBUG: 	loop_coverage_rate=1.5
    191. 

  191. [2024-08-27 15:46:09] DEBUG: 	repeat_edge_cov_mult=1.75
    192. 

  192. [2024-08-27 15:46:09] DEBUG: 	weak_detach_rate=5
    193. 

  193. [2024-08-27 15:46:09] DEBUG: 	tip_coverage_rate=2
    194. 

  194. [2024-08-27 15:46:09] DEBUG: 	tip_length_rate=2
    195. 

  195. [2024-08-27 15:46:09] DEBUG: 	output_gfa_before_rr=1
    196. 

  196. [2024-08-27 15:46:09] DEBUG: 	remove_alt_edges=0
    197. 

  197. [2024-08-27 15:46:09] DEBUG: 	low_cutoff_warning=0
    198. 

  198. [2024-08-27 15:46:09] DEBUG: 	kmer_size=17
    199. 

  199. [2024-08-27 15:46:09] DEBUG: 	use_minimizers=1
    200. 

  200. [2024-08-27 15:46:09] DEBUG: 	minimizer_window=10
    201. 

  201. [2024-08-27 15:46:09] DEBUG: 	reads_base_alignment=1
    202. 

  202. [2024-08-27 15:46:09] DEBUG: 	meta_read_top_kmer_rate=0.75
    203. 

  203. [2024-08-27 15:46:09] DEBUG: 	maximum_jump=1500
    204. 

  204. [2024-08-27 15:46:09] DEBUG: 	maximum_overhang=1500
    205. 

  205. [2024-08-27 15:46:09] DEBUG: 	repeat_kmer_rate=100
    206. 

  206. [2024-08-27 15:46:09] DEBUG: 	assemble_ovlp_divergence=0.05
    207. 

  207. [2024-08-27 15:46:09] DEBUG: 	assemble_divergence_relative=1
    208. 

  208. [2024-08-27 15:46:09] DEBUG: 	repeat_graph_ovlp_divergence=0.05
    209. 

  209. [2024-08-27 15:46:09] DEBUG: 	read_align_ovlp_divergence=0.10
    210. 

  210. [2024-08-27 15:46:09] DEBUG: 	hpc_scoring_on=1
    211. 

  211. [2024-08-27 15:46:09] DEBUG: 	add_unassembled_reads=0
    212. 

  212. [2024-08-27 15:46:09] DEBUG: 	extend_contigs_with_repeats=0
    213. 

  213. [2024-08-27 15:46:09] DEBUG: 	min_read_cov_cutoff=3
    214. 

  214. [2024-08-27 15:46:09] DEBUG: 	short_tip_length=20000
    215. 

  215. [2024-08-27 15:46:09] DEBUG: 	long_tip_length=100000
    216. 

  216. [2024-08-27 15:46:09] DEBUG: Running with k-mer size: 17
    217. 

  217. [2024-08-27 15:46:09] DEBUG: Selected minimum overlap 4000
    218. 

  218. [2024-08-27 15:46:09] DEBUG: Metagenome mode: N
    219. 

  219. [2024-08-27 15:46:09] INFO: Parsing disjointigs
    220. 

  220. [2024-08-27 15:46:09] DEBUG: Building positional index
    221. 

  221. [2024-08-27 15:46:09] DEBUG: Total sequence: 20438 bp
    222. 

  222. [2024-08-27 15:46:09] INFO: Building repeat graph
    223. 

  223. [2024-08-27 15:46:09] DEBUG: Mean k-mer frequency: 1.00242
    224. 

  224. [2024-08-27 15:46:09] DEBUG: Repetitive k-mer frequency: 100
    225. 

  225. [2024-08-27 15:46:09] DEBUG: Filtered 0 repetitive k-mers (0)
    226. 

  226. [2024-08-27 15:46:09] DEBUG: Sorting k-mer index
    227. 

  227. [2024-08-27 15:46:09] DEBUG: Selected k-mers: 3721
    228. 

  228. [2024-08-27 15:46:09] DEBUG: K-mer index size: 3731
    229. 

  229. [2024-08-27 15:46:09] DEBUG: Mean k-mer frequency: 1.00269
    230. 

  230. [2024-08-27 15:46:09] DEBUG: Minimizer rate: 5.47789
    231. 

  231. [2024-08-27 15:46:09] DEBUG: Computing transitive closure for overlaps
    232. 

  232. [2024-08-27 15:46:09] DEBUG: Found 0 overlaps
    233. 

  233. [2024-08-27 15:46:09] DEBUG: Left 0 overlaps after filtering
    234. 

  234. [2024-08-27 15:46:09] INFO: Median overlap divergence: 0
    235. 

  235. [2024-08-27 15:46:09] DEBUG: Sequence divergence distribution: 
    236. 

  236. 

  237.     |          |                                                                                         
    238. 

  238.     |          |                                                                                         
    239. 

  239.     |          |                                                                                         
    240. 

  240.     |          |                                                                                         
    241. 

  241.     |          |                                                                                         
    242. 

  242.     |          |                                                                                         
    243. 

  243.     |          |                                                                                         
    244. 

  244.     |          |                                                                                         
    245. 

  245.     |          |                                                                                         
    246. 

  246.     |          |                                                                                         
    247. 

  247.     |          |                                                                                         
    248. 

  248.     |          |                                                                                         
    249. 

  249.     |          |                                                                                         
    250. 

  250.     |          |                                                                                         
    251. 

  251.     |          |                                                                                         
    252. 

  252.     |          |                                                                                         
    253. 

  253.     |          |                                                                                         
    254. 

  254.     |          |                                                                                         
    255. 

  255.     |          |                                                                                         
    256. 

  256.     |          |                                                                                         
    257. 

  257.     ----------------------------------------------------------------------------------------------------
    258. 

  258.     0%        5%        10%       15%       20%       25%       30%       35%       40%       45%       
    259. 

  259. 

  260.     Q25 = 0, Q50 = 0, Q75 = 0
    261. 

  261. 

  262. [2024-08-27 15:46:09] DEBUG: Computing gluepoints
    263. 

  263. [2024-08-27 15:46:09] DEBUG: Added 0 gluepoint projections
    264. 

  264. [2024-08-27 15:46:09] DEBUG: Created 4 gluepoints
    265. 

  265. [2024-08-27 15:46:09] DEBUG: Artificial loops removed: 0 left, 0 right, 0 both
    266. 

  266. [2024-08-27 15:46:09] DEBUG: Initializing edges
    267. 

  267. [2024-08-27 15:46:09] DEBUG: Edges length checksum: 417670969
    268. 

  268. [2024-08-27 15:46:09] DEBUG: Filtered 0 singleton segments
    269. 

  269. [2024-08-27 15:46:09] DEBUG: Removed 0 simple and 0 double chimeric junctions
    270. 

  270. [2024-08-27 15:46:09] DEBUG: Collapsed 0 edges
    271. 

  271. [2024-08-27 15:46:09] DEBUG: *	1	+disjointig_1	0	20437	20437	
    272. 

  272. [2024-08-27 15:46:09] DEBUG: Total edges: 1
    273. 

  273. [2024-08-27 15:46:09] INFO: Parsing reads
    274. 

  274. [2024-08-27 15:46:09] DEBUG: Building positional index
    275. 

  275. [2024-08-27 15:46:09] DEBUG: Total sequence: 117213 bp
    276. 

  276. [2024-08-27 15:46:09] DEBUG: Building positional index
    277. 

  277. [2024-08-27 15:46:09] DEBUG: Total sequence: 20437 bp
    278. 

  278. [2024-08-27 15:46:09] INFO: Aligning reads to the graph
    279. 

  279. [2024-08-27 15:46:09] DEBUG: Mean k-mer frequency: 1.00242
    280. 

  280. [2024-08-27 15:46:09] DEBUG: Repetitive k-mer frequency: 100
    281. 

  281. [2024-08-27 15:46:09] DEBUG: Filtered 0 repetitive k-mers (0)
    282. 

  282. [2024-08-27 15:46:09] DEBUG: Sorting k-mer index
    283. 

  283. [2024-08-27 15:46:09] DEBUG: Selected k-mers: 3721
    284. 

  284. [2024-08-27 15:46:09] DEBUG: K-mer index size: 3731
    285. 

  285. [2024-08-27 15:46:09] DEBUG: Mean k-mer frequency: 1.00269
    286. 

  286. [2024-08-27 15:46:09] DEBUG: Minimizer rate: 5.47762
    287. 

  287. [2024-08-27 15:46:09] DEBUG: Total reads : 14
    288. 

  288. [2024-08-27 15:46:09] DEBUG: Read with aligned parts : 14
    289. 

  289. [2024-08-27 15:46:09] DEBUG: Aligned in one piece : 14
    290. 

  290. [2024-08-27 15:46:09] INFO: Aligned read sequence: 107454 / 113554 (0.946281)
    291. 

  291. [2024-08-27 15:46:09] INFO: Median overlap divergence: 0.00542122
    292. 

  292. [2024-08-27 15:46:09] DEBUG: Sequence divergence distribution: 
    293. 

  293. 

  294.     |**                  |                                                                               
    295. 

  295.     |**                  |                                                                               
    296. 

  296.     |**                  |                                                                               
    297. 

  297.     |**                  |                                                                               
    298. 

  298.     |**                  |                                                                               
    299. 

  299.     |**                  |                                                                               
    300. 

  300.     |**                  |                                                                               
    301. 

  301.     |**                  |                                                                               
    302. 

  302.     |**                  |                                                                               
    303. 

  303.     |**                  |                                                                               
    304. 

  304.     |**                  |                                                                               
    305. 

  305.     |**                  |                                                                               
    306. 

  306.     |**                  |                                                                               
    307. 

  307.     |**                  |                                                                               
    308. 

  308.     |**                  |                                                                               
    309. 

  309.     |**                  |                                                                               
    310. 

  310.     |****                |                                                                               
    311. 

  311.     |****                |                                                                               
    312. 

  312.     |****                |                                                                               
    313. 

  313.     |****                |                                                                               
    314. 

  314.     ----------------------------------------------------------------------------------------------------
    315. 

  315.     0%        5%        10%       15%       20%       25%       30%       35%       40%       45%       
    316. 

  316. 

  317.     Q25 = 0.0031, Q50 = 0.0054, Q75 = 0.0061
    318. 

  318. 

  319. [2024-08-27 15:46:09] INFO: Mean edge coverage: 5
    320. 

  320. [2024-08-27 15:46:09] DEBUG: 1	len:20437	cov:3	mult:0.6
    321. 

  321. [2024-08-27 15:46:09] DEBUG: -1	len:20437	cov:3	mult:0.6
    322. 

  322. [2024-08-27 15:46:09] DEBUG: Unique coverage threshold 5
    323. 

  323. [2024-08-27 15:46:09] INFO: Simplifying the graph
    324. 

  324. [2024-08-27 15:46:09] DEBUG: Read coverage cutoff: 3
    325. 

  325. [2024-08-27 15:46:09] DEBUG: [SIMPL] Removed 0 paths with low coverage
    326. 

  326. [2024-08-27 15:46:09] DEBUG: [SIMPL] Masked 0 heterozygous loops
    327. 

  327. [2024-08-27 15:46:09] DEBUG: [SIMPL] Masked 0 simple bubbles
    328. 

  328. [2024-08-27 15:46:09] DEBUG: Finding repeats
    329. 

  329. [2024-08-27 15:46:09] DEBUG: Read coverage cutoff: 3
    330. 

  330. [2024-08-27 15:46:09] DEBUG: Repeat detection iteration 1
    331. 

  331. [2024-08-27 15:46:09] DEBUG: Writing Dot
    332. 

  332. [2024-08-27 15:46:09] DEBUG: Writing FASTA
    333. 

  333. [2024-08-27 15:46:09] DEBUG: Writing Gfa
    334. 

  334. [2024-08-27 15:46:09] DEBUG: [SIMPL] == Iteration 1 ==
    335. 

  335. [2024-08-27 15:46:09] DEBUG: Splitting nodes
    336. 

  336. [2024-08-27 15:46:09] DEBUG: [SIMPL] Split 0 nodes
    337. 

  337. [2024-08-27 15:46:09] DEBUG: [SIMPL] Clipped 0 short and 0 long tips
    338. 

  338. [2024-08-27 15:46:09] DEBUG: [SIMPL] Masked 0 heterozygous loops
    339. 

  339. [2024-08-27 15:46:09] DEBUG: [SIMPL] Masked 0 simple bubbles
    340. 

  340. [2024-08-27 15:46:09] DEBUG: Finding repeats
    341. 

  341. [2024-08-27 15:46:09] DEBUG: Read coverage cutoff: 3
    342. 

  342. [2024-08-27 15:46:09] DEBUG: Repeat detection iteration 1
    343. 

  343. [2024-08-27 15:46:09] DEBUG: Total unique edges: 1
    344. 

  344. [2024-08-27 15:46:09] DEBUG: [SIMPL] Resolved repeats: 0
    345. 

  345. [2024-08-27 15:46:09] DEBUG: RR links: 0
    346. 

  346. [2024-08-27 15:46:09] DEBUG: Unresolved: 0
    347. 

  347. [2024-08-27 15:46:09] DEBUG: Removed 0 simple and 0 double chimeric junctions
    348. 

  348. [2024-08-27 15:46:09] DEBUG: [SIMPL] Collapsed 0 haplotypes
    349. 

  349. [2024-08-27 15:46:09] DEBUG: [SIMPL] Resolved 0 simple repeats
    350. 

  350. [2024-08-27 15:46:09] DEBUG: Read coverage cutoff: 3
    351. 

  351. [2024-08-27 15:46:09] DEBUG: [SIMPL] Removed 0 paths with low coverage
    352. 

  352. [2024-08-27 15:46:09] DEBUG: Finding repeats
    353. 

  353. [2024-08-27 15:46:09] DEBUG: Read coverage cutoff: 3
    354. 

  354. [2024-08-27 15:46:09] DEBUG: Repeat detection iteration 1
    355. 

  355. [2024-08-27 15:46:09] DEBUG: Writing Dot
    356. 

  356. [2024-08-27 15:46:09] DEBUG: Writing FASTA
    357. 

  357. [2024-08-27 15:46:09] DEBUG: Peak RAM usage: 0 Gb
    358. 

  358. -----------End assembly log------------
    359. 

  359. [2024-08-27 15:46:09] root: INFO: >>>STAGE: contigger
    360. 

  360. [2024-08-27 15:46:09] root: INFO: Generating contigs
    361. 

  361. [2024-08-27 15:46:09] root: DEBUG: -----Begin contigger analyser log------
    362. 

  362. [2024-08-27 15:46:09] root: DEBUG: Running: flye-modules contigger --graph-edges /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/20-repeat/repeat_graph_edges.fasta --reads /home/prom/Documents/Programmes/pandora_lib_assembler/output_7.fasta --out-dir /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/30-contigger --config /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg --repeat-graph /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/20-repeat/repeat_graph_dump --graph-aln /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/20-repeat/read_alignment_dump --log /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/flye.log --threads 1 --min-ovlp 4000
    363. 

  363. [2024-08-27 15:46:09] DEBUG: Build date: May 16 2023 00:48:47
    364. 

  364. [2024-08-27 15:46:09] DEBUG: Total RAM: 503 Gb
    365. 

  365. [2024-08-27 15:46:09] DEBUG: Available RAM: 420 Gb
    366. 

  366. [2024-08-27 15:46:09] DEBUG: Total CPUs: 160
    367. 

  367. [2024-08-27 15:46:09] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_nano_hq.cfg
    368. 

  368. [2024-08-27 15:46:09] DEBUG: Loading /data/tools/Flye/flye/config/bin_cfg/asm_defaults.cfg
    369. 

  369. [2024-08-27 15:46:09] DEBUG: 	big_genome_threshold=29000000
    370. 

  370. [2024-08-27 15:46:09] DEBUG: 	meta_read_filter_kmer_freq=100
    371. 

  371. [2024-08-27 15:46:09] DEBUG: 	chain_large_gap_penalty=2
    372. 

  372. [2024-08-27 15:46:09] DEBUG: 	chain_small_gap_penalty=0.5
    373. 

  373. [2024-08-27 15:46:09] DEBUG: 	chain_gap_jump_threshold=100
    374. 

  374. [2024-08-27 15:46:09] DEBUG: 	max_jump_gap=500
    375. 

  375. [2024-08-27 15:46:09] DEBUG: 	max_coverage_drop_rate=5
    376. 

  376. [2024-08-27 15:46:09] DEBUG: 	max_extensions_drop_rate=5
    377. 

  377. [2024-08-27 15:46:09] DEBUG: 	chimera_window=100
    378. 

  378. [2024-08-27 15:46:09] DEBUG: 	chimera_overhang=1000
    379. 

  379. [2024-08-27 15:46:09] DEBUG: 	min_reads_in_disjointig=4
    380. 

  380. [2024-08-27 15:46:09] DEBUG: 	max_inner_reads=10
    381. 

  381. [2024-08-27 15:46:09] DEBUG: 	max_inner_fraction=0.25
    382. 

  382. [2024-08-27 15:46:09] DEBUG: 	aggressive_dup_filter=1
    383. 

  383. [2024-08-27 15:46:09] DEBUG: 	max_separation=500
    384. 

  384. [2024-08-27 15:46:09] DEBUG: 	unique_edge_length=50000
    385. 

  385. [2024-08-27 15:46:09] DEBUG: 	min_repeat_res_support=0.51
    386. 

  386. [2024-08-27 15:46:09] DEBUG: 	out_paths_ratio=5
    387. 

  387. [2024-08-27 15:46:09] DEBUG: 	graph_cov_drop_rate=5
    388. 

  388. [2024-08-27 15:46:09] DEBUG: 	coverage_estimate_window=100
    389. 

  389. [2024-08-27 15:46:09] DEBUG: 	max_bubble_length=50000
    390. 

  390. [2024-08-27 15:46:09] DEBUG: 	loop_coverage_rate=1.5
    391. 

  391. [2024-08-27 15:46:09] DEBUG: 	repeat_edge_cov_mult=1.75
    392. 

  392. [2024-08-27 15:46:09] DEBUG: 	weak_detach_rate=5
    393. 

  393. [2024-08-27 15:46:09] DEBUG: 	tip_coverage_rate=2
    394. 

  394. [2024-08-27 15:46:09] DEBUG: 	tip_length_rate=2
    395. 

  395. [2024-08-27 15:46:09] DEBUG: 	output_gfa_before_rr=1
    396. 

  396. [2024-08-27 15:46:09] DEBUG: 	remove_alt_edges=0
    397. 

  397. [2024-08-27 15:46:09] DEBUG: 	low_cutoff_warning=0
    398. 

  398. [2024-08-27 15:46:09] DEBUG: 	kmer_size=17
    399. 

  399. [2024-08-27 15:46:09] DEBUG: 	use_minimizers=1
    400. 

  400. [2024-08-27 15:46:09] DEBUG: 	minimizer_window=10
    401. 

  401. [2024-08-27 15:46:09] DEBUG: 	reads_base_alignment=1
    402. 

  402. [2024-08-27 15:46:09] DEBUG: 	meta_read_top_kmer_rate=0.75
    403. 

  403. [2024-08-27 15:46:09] DEBUG: 	maximum_jump=1500
    404. 

  404. [2024-08-27 15:46:09] DEBUG: 	maximum_overhang=1500
    405. 

  405. [2024-08-27 15:46:09] DEBUG: 	repeat_kmer_rate=100
    406. 

  406. [2024-08-27 15:46:09] DEBUG: 	assemble_ovlp_divergence=0.05
    407. 

  407. [2024-08-27 15:46:09] DEBUG: 	assemble_divergence_relative=1
    408. 

  408. [2024-08-27 15:46:09] DEBUG: 	repeat_graph_ovlp_divergence=0.05
    409. 

  409. [2024-08-27 15:46:09] DEBUG: 	read_align_ovlp_divergence=0.10
    410. 

  410. [2024-08-27 15:46:09] DEBUG: 	hpc_scoring_on=1
    411. 

  411. [2024-08-27 15:46:09] DEBUG: 	add_unassembled_reads=0
    412. 

  412. [2024-08-27 15:46:09] DEBUG: 	extend_contigs_with_repeats=0
    413. 

  413. [2024-08-27 15:46:09] DEBUG: 	min_read_cov_cutoff=3
    414. 

  414. [2024-08-27 15:46:09] DEBUG: 	short_tip_length=20000
    415. 

  415. [2024-08-27 15:46:09] DEBUG: 	long_tip_length=100000
    416. 

  416. [2024-08-27 15:46:09] DEBUG: Running with k-mer size: 17
    417. 

  417. [2024-08-27 15:46:09] DEBUG: Selected minimum overlap 4000
    418. 

  418. [2024-08-27 15:46:09] INFO: Reading sequences
    419. 

  419. [2024-08-27 15:46:09] DEBUG: Building positional index
    420. 

  420. [2024-08-27 15:46:09] DEBUG: Total sequence: 117213 bp
    421. 

  421. [2024-08-27 15:46:09] DEBUG: Flipped 0
    422. 

  422. [2024-08-27 15:46:09] DEBUG: UPath 1: 1
    423. 

  423. [2024-08-27 15:46:09] DEBUG: Final graph contains 1 egdes
    424. 

  424. [2024-08-27 15:46:09] DEBUG: Extending contigs into repeats
    425. 

  425. [2024-08-27 15:46:09] DEBUG: Covered 0 repetitive contigs
    426. 

  426. [2024-08-27 15:46:09] INFO: Generated 1 contigs
    427. 

  427. [2024-08-27 15:46:09] DEBUG: Writing FASTA
    428. 

  428. [2024-08-27 15:46:09] DEBUG: Generating scaffold connections
    429. 

  429. [2024-08-27 15:46:09] INFO: Added 0 scaffold connections
    430. 

  430. [2024-08-27 15:46:09] DEBUG: Writing Dot
    431. 

  431. [2024-08-27 15:46:09] DEBUG: Writing FASTA
    432. 

  432. [2024-08-27 15:46:09] DEBUG: Writing Gfa
    433. 

  433. [2024-08-27 15:46:09] DEBUG: Peak RAM usage: 0 Gb
    434. 

  434. -----------End assembly log------------
    435. 

  435. [2024-08-27 15:46:09] root: INFO: >>>STAGE: polishing
    436. 

  436. [2024-08-27 15:46:09] root: INFO: Polishing genome (1/1)
    437. 

  437. [2024-08-27 15:46:09] root: INFO: Running minimap2
    438. 

  438. [2024-08-27 15:46:09] root: INFO: Separating alignment into bubbles
    439. 

  439. [2024-08-27 15:46:10] root: DEBUG: Generated 1204 bubbles
    440. 

  440. [2024-08-27 15:46:10] root: DEBUG: Split 0 long bubbles
    441. 

  441. [2024-08-27 15:46:10] root: DEBUG: Skipped 0 empty bubbles
    442. 

  442. [2024-08-27 15:46:10] root: DEBUG: Skipped 0 bubbles with long branches
    443. 

  443. [2024-08-27 15:46:10] root: INFO: Alignment error rate: 0.007978
    444. 

  444. [2024-08-27 15:46:10] root: INFO: Correcting bubbles
    445. 

  445. [2024-08-27 15:46:10] root: DEBUG: Mean contig coverage: 3, selected threshold: 3
    446. 

  446. [2024-08-27 15:46:10] root: DEBUG: Filtered 0 contigs of total length 0
    447. 

  447. [2024-08-27 15:46:10] root: DEBUG: Generating polished GFA
    448. 

  448. [2024-08-27 15:46:10] root: DEBUG: 0 sequences remained unpolished
    449. 

  449. [2024-08-27 15:46:10] root: INFO: >>>STAGE: finalize
    450. 

  450. [2024-08-27 15:46:10] root: DEBUG: ---Output dir contents:----
    451. 

  451. [2024-08-27 15:46:10] root: DEBUG: tmp_7/
    452. 

  452. [2024-08-27 15:46:10] root: DEBUG:     363.0 B     assembly_graph.gv
    453. 

  453. [2024-08-27 15:46:10] root: DEBUG:     28.0 K      flye.log
    454. 

  454. [2024-08-27 15:46:10] root: DEBUG:     20.0 K      assembly_graph.gfa
    455. 

  455. [2024-08-27 15:46:10] root: DEBUG:     20.0 K      assembly.fasta
    456. 

  456. [2024-08-27 15:46:10] root: DEBUG:     92.0 B      params.json
    457. 

  457. [2024-08-27 15:46:10] root: DEBUG:     10-consensus/
    458. 

  458. [2024-08-27 15:46:10] root: DEBUG:         902.0 B     minimap.stderr
    459. 

  459. [2024-08-27 15:46:10] root: DEBUG:         104.0 B     minimap.bam.bai
    460. 

  460. [2024-08-27 15:46:10] root: DEBUG:         20.0 K      consensus.fasta
    461. 

  461. [2024-08-27 15:46:10] root: DEBUG:     00-assembly/
    462. 

  462. [2024-08-27 15:46:10] root: DEBUG:         28.0 B      draft_assembly.fasta.fai
    463. 

  463. [2024-08-27 15:46:10] root: DEBUG:         20.0 K      draft_assembly.fasta
    464. 

  464. [2024-08-27 15:46:10] root: DEBUG:     30-contigger/
    465. 

  465. [2024-08-27 15:46:10] root: DEBUG:         24.0 B      contigs.fasta.fai
    466. 

  466. [2024-08-27 15:46:10] root: DEBUG:         0.0 B       scaffolds_links.txt
    467. 

  467. [2024-08-27 15:46:10] root: DEBUG:         20.0 K      graph_final.gfa
    468. 

  468. [2024-08-27 15:46:10] root: DEBUG:         20.0 K      graph_final.fasta
    469. 

  469. [2024-08-27 15:46:10] root: DEBUG:         109.0 B     contigs_stats.txt
    470. 

  470. [2024-08-27 15:46:10] root: DEBUG:         363.0 B     graph_final.gv
    471. 

  471. [2024-08-27 15:46:10] root: DEBUG:         20.0 K      contigs.fasta
    472. 

  472. [2024-08-27 15:46:10] root: DEBUG:     20-repeat/
    473. 

  473. [2024-08-27 15:46:10] root: DEBUG:         3.0 K       read_alignment_dump
    474. 

  474. [2024-08-27 15:46:10] root: DEBUG:         363.0 B     graph_before_rr.gv
    475. 

  475. [2024-08-27 15:46:10] root: DEBUG:         20.0 K      graph_before_rr.fasta
    476. 

  476. [2024-08-27 15:46:10] root: DEBUG:         173.0 B     repeat_graph_dump
    477. 

  477. [2024-08-27 15:46:10] root: DEBUG:         363.0 B     graph_after_rr.gv
    478. 

  478. [2024-08-27 15:46:10] root: DEBUG:         19.0 K      graph_before_rr.gfa
    479. 

  479. [2024-08-27 15:46:10] root: DEBUG:         20.0 K      repeat_graph_edges.fasta
    480. 

  480. [2024-08-27 15:46:10] root: DEBUG:     40-polishing/
    481. 

  481. [2024-08-27 15:46:10] root: DEBUG:         20.0 K      filtered_contigs.fasta
    482. 

  482. [2024-08-27 15:46:10] root: DEBUG:         926.0 B     minimap.stderr
    483. 

  483. [2024-08-27 15:46:10] root: DEBUG:         24.0 B      filtered_contigs.fasta.fai
    484. 

  484. [2024-08-27 15:46:10] root: DEBUG:         43.0 B      contigs_stats.txt
    485. 

  485. [2024-08-27 15:46:10] root: DEBUG:         104.0 B     minimap_1.bam.bai
    486. 

  486. [2024-08-27 15:46:10] root: DEBUG:         104.0 B     edges_aln.bam.bai
    487. 

  487. [2024-08-27 15:46:10] root: DEBUG:         20.0 K      polished_edges.gfa
    488. 

  488. [2024-08-27 15:46:10] root: DEBUG:         5.0 K       base_coverage.bed.gz
    489. 

  489. [2024-08-27 15:46:10] root: DEBUG:         43.0 B      filtered_stats.txt
    490. 

  490. [2024-08-27 15:46:10] root: DEBUG: --------------------------
    491. 

  491. [2024-08-27 15:46:10] root: INFO: Assembly statistics:
    492. 

  492. 

  493. 	Total length:	20439
    494. 

  494. 	Fragments:	1
    495. 

  495. 	Fragments N50:	20439
    496. 

  496. 	Largest frg:	20439
    497. 

  497. 	Scaffolds:	0
    498. 

  498. 	Mean coverage:	3
    499. 

  499. 

  500. [2024-08-27 15:46:10] root: INFO: Final assembly: /home/prom/Documents/Programmes/pandora_lib_assembler/tmp_7/assembly.fasta
    501.